Mercurial > repos > jackcurragh > ribogalaxy_bowtie_genome

comparison bowtie_genome_wrapper/bowtie_genomic_wrapper.xml @ 9:5b1395ac1501 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jackcurragh
date Fri, 13 May 2022 09:31:48 +0000
parents 12688201bbe8
children 5b0c7db21414
comparison
equal deleted inserted replaced
8:fe590b3f8b1a 9:5b1395ac1501
1 <tool id="bowtie_genomic_wrapper" name="Align to the Genome with Bowtie" version="1.2.0"> 1 <tool id="bowtie_genomic_wrapper" name="Bowtie Genome Alignment" version="1.3.0">
2 <description></description> 2 <description>Align to the Genome with Bowtie</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.2.0">bowtie</requirement> 4 <requirement type="package" version="1.2.0">bowtie</requirement>
5 <requirement type="package" version="1.13">samtools</requirement>
6
5 </requirements> 7 </requirements>
6 <version_command>bowtie --version</version_command> 8 <version_command>bowtie --version</version_command>
7 <command> 9 <command>
8 python '$__tool_directory__/bowtie_genomic_wrapper.py' 10 python '$__tool_directory__/bowtie_genomic_wrapper.py'
9 ## Set number of threads 11 ## Set number of threads
158 <option value="indexed">Use a built-in index</option> 160 <option value="indexed">Use a built-in index</option>
159 <option value="history">Use one from the history</option> 161 <option value="history">Use one from the history</option>
160 </param> 162 </param>
161 <when value="indexed"> 163 <when value="indexed">
162 <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> 164 <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
163 <options from_data_table="bowtie_genome_indexes"> 165 <options from_data_table="bowtie_indexes">
164 <filter type="sort_by" column="2" /> 166 <filter type="sort_by" column="2" />
165 <validator type="no_options" message="No indexes are available" /> 167 <validator type="no_options" message="No indexes are available" />
166 </options> 168 </options>
167 </param> 169 </param>
168 </when> 170 </when>
425 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> 427 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
426 <actions> 428 <actions>
427 <conditional name="refGenomeSource.genomeSource"> 429 <conditional name="refGenomeSource.genomeSource">
428 <when value="indexed"> 430 <when value="indexed">
429 <action type="metadata" name="dbkey"> 431 <action type="metadata" name="dbkey">
430 <option type="from_data_table" name="bowtie_genome_indexes" column="1" offset="0"> 432 <option type="from_data_table" name="bowtie_indexes" column="1" offset="0">
431 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> 433 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
432 <filter type="param_value" ref="refGenomeSource.index" column="0"/> 434 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
433 </option> 435 </option>
434 </action> 436 </action>
435 </when> 437 </when>
543 bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam 545 bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam
544 sort bowtie_out6_u.sam > bowtie_out6.sam 546 sort bowtie_out6_u.sam > bowtie_out6.sam
545 -p is the number of threads. You need to replace the + with 2 dashes. 547 -p is the number of threads. You need to replace the + with 2 dashes.
546 chrM_base needs to be the base location/name of the index files. 548 chrM_base needs to be the base location/name of the index files.
547 --> 549 -->
548 <param name="genomeSource" value="indexed" /> 550 <param name="genomeSource" value="history" />
549 <!-- this is the backwards-compatible "unique value" for this index, not an actual path --> 551 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
550 <param name="index" value="equCab2chrM" /> 552 <param name="ownFile" value="Homo_sapiens.GRCh38.dna.chromosome.9.fa" />
551 <param name="sPaired" value="single" /> 553 <param name="sPaired" value="single" />
552 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" /> 554 <param name="sInput1" ftype="fastqsanger" value="sampled_fq.fastq.fastq" />
553 <param name="sSettingsType" value="preSet" />
554 <param name="suppressHeader" value="true" />
555 <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True">
556 <metadata name="dbkey" value="equCab2" />
557 </output>
558 </test>
559 <test>
560 <!--
561 Bowtie command:
562 bowtie-build -f test-data/phiX.fasta phiX_base
563 bowtie -q -X 1000 +ff -p 4 -S +sam-nohead -n 2 -e 70 -l 28 +pairtries 100 +maxbts 800 +best +un bowtie_out8_u.fastq phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out7_u.sam
564 sort bowtie_out7_u.sam > bowtie_out7.sam
565 sort bowtie_out8_u_1.sam > bowtie_out8_1.sam
566 sort bowtie_out8_u_2.sam > bowtie_out8_2.sam
567 Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines.
568 -p is the number of threads. You need to replace the + with 2 dashes.
569 The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq.
570 chrM_base is the index files' location/base name.
571 -->
572 <param name="genomeSource" value="history" />
573 <param name="ownFile" value="phiX.fasta" />
574 <param name="indexSettings" value="indexPreSet" />
575 <param name="sPaired" value="paired" />
576 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
577 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
578 <param name="pMaxInsert" value="1000" />
579 <param name="pMateOrient" value="ff" />
580 <param name="pSettingsType" value="full" />
581 <param name="pSkip" value="0" />
582 <param name="pAlignLimit" value="-1" />
583 <param name="pTrimH" value="0" />
584 <param name="pTrimL" value="0" />
585 <param name="alignMode" value="nMode" />
586 <param name="pMismatchSeed" value="2" />
587 <param name="pMismatchQual" value="70" />
588 <param name="pSeedLen" value="28" />
589 <param name="pRounding" value="round" />
590 <param name="pMinInsert" value="0" />
591 <param name="pMaxAlignAttempt" value="100" />
592 <param name="pForwardAlign" value="forward" />
593 <param name="pReverseAlign" value="reverse" />
594 <param name="pTryHard" value="noTryHard" />
595 <param name="pValAlign" value="1" />
596 <param name="pAllValAligns" value="noAllValAligns" />
597 <param name="pSuppressAlign" value="-1" />
598 <param name="pUnmappedFile" value="true" />
599 <param name="pMaxFile" value="false" />
600 <param name="pBest" value="doBest" />
601 <param name="pdMaxBacktracks" value="800" />
602 <param name="pdStrata" value="noStrata" />
603 <param name="pOffrate" value="-1" />
604 <param name="pSeed" value="-1" />
605 <param name="suppressHeader" value="true" />
606 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
607 <output name="output_unmapped_reads_l" ftype="fastqsanger" file="bowtie_out8_1.fastq" sort="True" />
608 <output name="output_unmapped_reads_r" ftype="fastqsanger" file="bowtie_out8_2.fastq" sort="True" />
609 </test>
610 <!-- start testing of non-sanger variant fastq reads -->
611 <test>
612 <param name="genomeSource" value="history" />
613 <param name="ownFile" value="phiX.fasta" />
614 <param name="indexSettings" value="indexPreSet" />
615 <param name="sPaired" value="paired" />
616 <param name="pInput1" ftype="fastqillumina" value="bowtie_in5.fastqillumina" />
617 <param name="pInput2" ftype="fastqillumina" value="bowtie_in6.fastqillumina" />
618 <param name="pMaxInsert" value="1000" />
619 <param name="pMateOrient" value="ff" />
620 <param name="pSettingsType" value="full" />
621 <param name="pSkip" value="0" />
622 <param name="pAlignLimit" value="-1" />
623 <param name="pTrimH" value="0" />
624 <param name="pTrimL" value="0" />
625 <param name="alignMode" value="nMode" />
626 <param name="pMismatchSeed" value="2" />
627 <param name="pMismatchQual" value="70" />
628 <param name="pSeedLen" value="28" />
629 <param name="pRounding" value="round" />
630 <param name="pMinInsert" value="0" />
631 <param name="pMaxAlignAttempt" value="100" />
632 <param name="pForwardAlign" value="forward" />
633 <param name="pReverseAlign" value="reverse" />
634 <param name="pTryHard" value="noTryHard" />
635 <param name="pValAlign" value="1" />
636 <param name="pAllValAligns" value="noAllValAligns" />
637 <param name="pSuppressAlign" value="-1" />
638 <param name="pUnmappedFile" value="true" />
639 <param name="pMaxFile" value="false" />
640 <param name="pBest" value="doBest" />
641 <param name="pdMaxBacktracks" value="800" />
642 <param name="pdStrata" value="noStrata" />
643 <param name="pOffrate" value="-1" />
644 <param name="pSeed" value="-1" />
645 <param name="suppressHeader" value="true" />
646 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
647 <output name="output_unmapped_reads_l" ftype="fastqillumina" file="bowtie_out8_1.fastqillumina.sorted" sort="True" />
648 <output name="output_unmapped_reads_r" ftype="fastqillumina" file="bowtie_out8_2.fastqillumina.sorted" sort="True" />
649 </test>
650 <test>
651 <param name="genomeSource" value="history" />
652 <param name="ownFile" value="phiX.fasta" />
653 <param name="indexSettings" value="indexPreSet" />
654 <param name="sPaired" value="paired" />
655 <param name="pInput1" ftype="fastqsolexa" value="bowtie_in5.fastqsolexa" />
656 <param name="pInput2" ftype="fastqsolexa" value="bowtie_in6.fastqsolexa" />
657 <param name="pMaxInsert" value="1000" />
658 <param name="pMateOrient" value="ff" />
659 <param name="pSettingsType" value="full" />
660 <param name="pSkip" value="0" />
661 <param name="pAlignLimit" value="-1" />
662 <param name="pTrimH" value="0" />
663 <param name="pTrimL" value="0" />
664 <param name="alignMode" value="nMode" />
665 <param name="pMismatchSeed" value="2" />
666 <param name="pMismatchQual" value="70" />
667 <param name="pSeedLen" value="28" />
668 <param name="pRounding" value="round" />
669 <param name="pMinInsert" value="0" />
670 <param name="pMaxAlignAttempt" value="100" />
671 <param name="pForwardAlign" value="forward" />
672 <param name="pReverseAlign" value="reverse" />
673 <param name="pTryHard" value="noTryHard" />
674 <param name="pValAlign" value="1" />
675 <param name="pAllValAligns" value="noAllValAligns" />
676 <param name="pSuppressAlign" value="-1" />
677 <param name="pUnmappedFile" value="true" />
678 <param name="pMaxFile" value="false" />
679 <param name="pBest" value="doBest" />
680 <param name="pdMaxBacktracks" value="800" />
681 <param name="pdStrata" value="noStrata" />
682 <param name="pOffrate" value="-1" />
683 <param name="pSeed" value="-1" />
684 <param name="suppressHeader" value="true" />
685 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
686 <output name="output_unmapped_reads_l" ftype="fastqsolexa" file="bowtie_out8_1.fastqsolexa.sorted" sort="True" />
687 <output name="output_unmapped_reads_r" ftype="fastqsolexa" file="bowtie_out8_2.fastqsolexa.sorted" sort="True" />
688 </test>
689 <!-- end testing of non-sanger variant fastq reads -->
690 <test>
691 <!--
692 Bowtie command:
693 bowtie -q -p 4 -S +sam-nohead -n 2 -e 70 -l 28 -y -k 1 chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out9_u.sam
694 sort bowtie_out9_u.sam > bowtie_out9.sam
695 -p is the number of threads. You need to replace the + with 2 dashes.
696 chrM_base is the index files' location/base name.
697 -->
698 <param name="genomeSource" value="indexed" />
699 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
700 <param name="index" value="equCab2chrM" />
701 <param name="sPaired" value="single" />
702 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
703 <param name="sSettingsType" value="full" /> 555 <param name="sSettingsType" value="full" />
704 <param name="sSkip" value="0" /> 556 <param name="sSuppressAlign" value='1' />
705 <param name="sAlignLimit" value="-1" /> 557 <param name="alignMode" value='nMode' />
706 <param name="sTrimH" value="0" /> 558 <param name="pMismatchSeed" value='1' />
707 <param name="sTrimL" value="0" /> 559
708 <param name="alignMode" value="nMode" /> 560
709 <param name="sMismatchSeed" value="2" /> 561 <output name="output" ftype="bam" file="test.bam"/>
710 <param name="sMismatchQual" value="70" />
711 <param name="sSeedLen" value="28" />
712 <param name="sRounding" value="round" />
713 <param name="sForwardAlign" value="forward" />
714 <param name="sReverseAlign" value="reverse" />
715 <param name="sTryHard" value="doTryHard" />
716 <param name="sValAlign" value="1" />
717 <param name="sAllValAligns" value="noAllValAligns" />
718 <param name="sSuppressAlign" value="-1" />
719 <param name="sUnmappedFile" value="false" />
720 <param name="sMaxFile" value="false" />
721 <param name="sBest" value="noBest" />
722 <param name="sOffrate" value="-1" />
723 <param name="sSeed" value="-1" />
724 <param name="suppressHeader" value="true" />
725 <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True">
726 <metadata name="dbkey" value="equCab2" />
727 </output>
728 </test>
729 <test>
730 <!--
731 Bowtie command:
732 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
733 bowtie -q -X 1000 +ff -p 4 -S +sam-nohead phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out10_u.sam
734 sort bowtie_out10_u.sam > bowtie_out10.sam
735 -p is the number of threads. You need to replace the + with 2 dashes.
736 chrM_base is the index files' location/base name.
737 -->
738 <param name="genomeSource" value="history" />
739 <param name="ownFile" value="phiX.fasta" />
740 <param name="indexSettings" value="indexFull" />
741 <param name="autoB" value="auto" />
742 <param name="nodc" value="dc" />
743 <param name="noref" value="ref" />
744 <param name="offrate" value="5" />
745 <param name="ftab" value="10" />
746 <param name="ntoa" value="no" />
747 <param name="endian" value="little" />
748 <param name="seed" value="-1" />
749 <param name="sPaired" value="paired" />
750 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
751 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
752 <param name="pMaxInsert" value="1000" />
753 <param name="pMateOrient" value="ff" />
754 <param name="pSettingsType" value="preSet" />
755 <param name="suppressHeader" value="true" />
756 <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
757 </test>
758 <test>
759 <!--
760 Bowtie command:
761 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
762 bowtie -q -X 1000 +ff -p 4 -S +sam-nohead phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out10_u.sam
763 sort bowtie_out10_u.sam > bowtie_out10.sam
764 -p is the number of threads. You need to replace the + with 2 dashes.
765 chrM_base is the index files' location/base name.
766 -->
767 <param name="genomeSource" value="history" />
768 <param name="ownFile" value="phiX.fasta" />
769 <param name="indexSettings" value="indexFull" />
770 <param name="autoB" value="auto" />
771 <param name="nodc" value="dc" />
772 <param name="noref" value="ref" />
773 <param name="offrate" value="5" />
774 <param name="ftab" value="10" />
775 <param name="ntoa" value="no" />
776 <param name="endian" value="little" />
777 <param name="seed" value="-1" />
778 <param name="sPaired" value="paired" />
779 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
780 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
781 <param name="pMaxInsert" value="1000" />
782 <param name="pMateOrient" value="ff" />
783 <param name="pSettingsType" value="preSet" />
784 <param name="suppressHeader" value="true" />
785 <param name="save_mapping_stats" value="true" />
786 <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
787 <output name="mapping_stats" ftype="txt" file="bowtie_out11.txt" sort="True" />
788 </test> 562 </test>
789 </tests> 563 </tests>
790 564
791 <help> 565 <help>
792 566